Tables

Tables or dataframes can be displayed in their tabular form by either printing a dataframe that is in the R environmnet, or by using one of several packages for creating customizable tables like the kable() function in the knitr package or the DT package for accessing the data.tables library

library(knitr)
kable(head(mtcars))

Graphs

Any graphical outputs from evaluated code chunks will appear in-line as they appear in the document. When outputting to an HTML document it is possible to include interactive plots like those available from the plotly package.

library(tidyverse)
library(plotly)

p <- ggplot(mtcars, aes(x = hp, y = mpg)) + 
  geom_point(aes(color = factor(cyl))) + 
  geom_smooth(aes(color = factor(cyl)), 
              method = "lm", se = FALSE)
ggplotly(p)

Formulas

In line formulas are written between single dollar \((\$)\) signs. Done this way the “von Bert” formula \(l_t = L_{\infty}(1-e^{-K(t-t_0)})\) will appear beside normal text. The formula notation in R Markdown follows LaTeX notation which makes adding special symbols as simple as looking them up here

Formulas can also be displayed out of text by bracketing with double dollar \((\$\$)\) signs : \[l_t = L_\infty(1-e^{-K(t-t_0)}) \]

You can also use math environments inside these closures to allow for matrix notation e.g., \[\begin{array}{ccc} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{array}\]

Maps

If the selected output type for your rmarkdown document is HTML (the default option), it will be possible to include interactive displays like zoomable maps/plots and searchable tables in your document.

library(leaflet)

m <- leaflet() %>% 
  addTiles() %>% # Add default OpenStreetMap map tiles
  setView(-88.943634, 30.441863, zoom = 16) %>% 
  addMarkers(lng = -88.943634, lat = 30.441863,
    popup="Oh look, Its us!")
m

Installation

Assuming that both R and Rstudio have been installed, users only need to install the “Rmarkdown” package from CRAN to begin creating html/word documents. In order to create pdf documents directly from Rstudio using R Markdown, users will need to install a distribution of LaTeX.

A full installation of LaTeX is rather large, and the authors of R Markdown and myself would strongly suggest installing tinytex as an alternative.

# Install from CRAN
install.packages('rmarkdown')

install.packages("tinytex")
tinytex::install_tinytex()  # install TinyTeX

Structure of an R Markdown Document

Most R Markdown documents are composed of three parts:

1. The YAML metadata found at the top of the document
2. The body, composed of text, divided by headers
3. Code blocks, these can be run to provide processed results, and/or shown as static text

---
title: "Rmarkdown Guide"
author: "Adam A. Kemberling"
date: "12/17/2018"
output: 
  html_document:
    toc: true
    toc_float: true
---

---
title: "Multiple Columns"
output: flexdashboard::flex_dashboard
---
    
Column {data-width=600}
-------------------------------------
    
### Chart 1

  ## R code for Chart 1          
#```{r}
#
#```
   
Column {data-width=400}
-------------------------------------
   
### Chart 2

## R code for Chart 2        
#```{r}
#
#```   
 
### Chart 3

## R code for Chart 3      
#```{r}
#
#```

Adding HTML/CSS directly into your rmarkdown document

CSS or html can be added directly into your rmarkdown using code chunks and the HTML() function in the htmltools package.

The code chunk below is html code used to change the style of div containers of the class “.header_1_class” by changing the background color to light blue, the border radius to 5 pixels, and the padding to 20 pixels. It also changes the background color of containers with the ID of “#header_1_id”. The class is “.header_1_class” because I named it that, you can name the class whatever you want, but it is easier to keep track of the classes if their names are meaningful. The css has to reference an object in your html document to do anything.

Alternatively you can put the exact same code in your stylesheet, and then just label your sections correctly in the rmarkdown file to have the same effect. It may be preferable to enter any “code” within a code chunk for the visual distinction when writing your .Rmnd files.

htmltools::HTML(
  '
<style>

/* Set A Style for a Specific Class */
.header_1_class { background-color:#e6f0ff; 
                  border-radius: 5px; 
                  padding: 20px;}
                  
/* Set A Style for a Specific ID */
#header_1_id { background-color: #ACACAC;}
</style>
'
)

The below sections will have style applied to them because the headers have been given ID and class labels “#header_1_id” & “.header_1_class”, which I set with # Identifying sections by their ID {#header_1_id} & # Identifying Sections by their class {.header_1_class}

htmltools::HTML(
  '
  <table style="width:100%">
  <tr>
    <th>Firstname</th>
    <th>Lastname</th> 
    <th>Age</th>
  </tr>
  <tr>
    <td>Jill</td>
    <td>Smith</td> 
    <td>50</td>
  </tr>
  <tr>
    <td>Eve</td>
    <td>Jackson</td> 
    <td>94</td>
  </tr>
</table>

<br/>
  '
)